You may consider to use following to get the latest 3.3.
cvs -z3 -d :pserver:[EMAIL PROTECTED]:/home/gmx/cvs login
cvs -z3 -d :pserver:[EMAIL PROTECTED]:/home/gmx/cvs co -r
release-3-3-patches gmx
Yang Ye
STEVENAZZI ANDREA wrote:
Dear David
I am desperate actually and would appreciate a lot if you could send me the
dihres.c that works with version 3.2.
Just in case is not so clear how to add the right lines in the topology file by
reading the code would you please suggest it to me too?
Thanks a lot
Best regards
Andrea
Andrea Stevenazzi
Medicinal & Computer Chemistry
Italfarmaco Research Centre
Italfarmaco SpA
Via dei Lavoratori 54
20092 Cinisello Balsamo
Milan
E-mail: [EMAIL PROTECTED]
Tel: +39-02-64433097
-----Messaggio originale-----
Da: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Per conto di David Mobley
Inviato: giovedì 16 marzo 2006 0.59
A: Discussion list for GROMACS users
Oggetto: Re: R: [gmx-users] Dihedral restraints
Regarding dihedral restraints in 3.2, the dihres.c section of code
only was a placeholder in 3.2 (it printed out "dihedral restraints on"
but the dihedral restraints did nothing) but was fixed (sort of)
before release of 3.3. I think the forces were still wrong in t he 3.3
release, though, so even if you get 3.3 working, you will probably
need to get the fixed dihres.c.
I do, however, probably have a dihres.c floating around somewhere that
would work properly with 3.3, and possibly also with 3.2 (at one point
David van der Spoel wrote the section of code after I discovered it
was missing from the 3.2 release). If you are desperate I can dig
around for it.
Thanks,
David
On 3/15/06, David van der Spoel <[EMAIL PROTECTED]> wrote:
STEVENAZZI ANDREA wrote:
Dear David
I did check the mailing list archives and could not find anything
related to.
Moreover, I have experienced some problems with version 3.3 of Gromacs
related to PME (see the mailing list archives) and I was forced to
install the 3.2.1 version in order to run a simulation.
There is a workaround for this too on the ftp site.
So you are telling me that dihedral restraints can not be set up in the
3.2 version?
Don't recall but probably not.
I beg you pardon if these are stupid questions, but I have started to
use Gromacs just 2 weeks ago.
Thanks
Andrea
STEVENAZZI ANDREA wrote:
Dear Gromacs Users
I am trying to use Gromacs for the MD of a small modified peptide
(just
4 residues with one ethylated) and I would like to set up one dihedral
restraint in the topology file.
I have not found anything useful on the paper manual regarding
dihedral
restraints and thought that it might not be possible to set them.
However, analysing the mdout.mdp file I realised that the keyword
dihre
(dihedral angle restraints) is actually there and can be turned on.
If that is true, does anybody know the right lines to insert in the
topology file in order to set properly a dihedral restraints?
Thanks
manual is a bit outdated. check mailing list archives. it is possible
with 3.3
Best regards
Andrea
Andrea Stevenazzi
Medicinal & Computer Chemistry
Italfarmaco Research Centre
Italfarmaco SpA
Via dei Lavoratori 54
20092 Cinisello Balsamo
Milan
E-mail: [EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>
Tel: +39-02-64433097
------------------------------------------------------------------------
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--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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